About 'empty folders' I had a similar problem a few month ago, it was caused by 'Firefox sync' .
About 'ctrl+shift+z' I will take a look.

Thank you for you feed back.

Edit:
In 0.7.12, I have the shortcut from 'Ctrl + Shift + Z' to 'Ctrl+Shit+U' (because 'Ctrl + Shift + Z' was interfering with Firefox shortcut 'Ctrl + Shift + Z': Redo)